Archive BacDiveID:10.13145/bacdive23113.20230509.8.1

Strain identifier

BacDive ID: 23113

Type strain:

Species: Actinoplanes rishiriensis

Strain Designation: RI50-RCA114

Strain history: <- C Suriyachadkun, BCC; BCC 49184 <- Y. Sakuraki

NCBI tax ID(s): 1050105 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 19173

BacDive-ID: 23113

DSM-Number: 45866

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Actinoplanes rishiriensis RI50-RCA114 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax id: 1050105
Matching level: species

strain history

@ref: 19173
history: <- C Suriyachadkun, BCC; BCC 49184 <- Y. Sakuraki

doi: 10.13145/bacdive23113.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Micromonosporales
family: Micromonosporaceae
genus: Actinoplanes
species: Actinoplanes rishiriensis
full scientific name: Actinoplanes rishiriensis Yamamura et al. 2012

@ref: 19173

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes rishiriensis

full scientific name: Actinoplanes rishiriensis Yamamura et al. 2012

strain designation: RI50-RCA114

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

multimedia

@ref	multimedia content	caption	intellectual property rights
19173	https://www.dsmz.de/microorganisms/photos/DSM_45866.jpg	Medium 553 28°C	© Leibniz-Institut DSMZ
19173	https://www.dsmz.de/microorganisms/photos/DSM_45866.jpg	Medium 65 28°C	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
19173	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
19173	GPHF-MEDIUM (DSMZ Medium 553)	yes	https://mediadive.dsmz.de/medium/553	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

culture temp

@ref: 19173
growth: positive
type: growth
temperature: 28
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	yes	95
69480	yes	100

Isolation, sampling and environmental information

isolation

@ref: 19173
sample type: soil
geographic location: Rishiri Island, Hokkaido
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_63249.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3725;97_24305;98_34654;99_63249&stattab=map
Last taxonomy: Actinoplanes rishiriensis
16S sequence: AB641831
Sequence Identity:
Total samples: 57
soil counts: 47
aquatic counts: 2
animal counts: 5
plant counts: 3

Safety information

risk assessment

@ref: 19173
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 19173
description: Actinoplanes rishiriensis gene for 16S rRNA, partial sequence
accession: AB641831
length: 1477
database: ena
NCBI tax ID: 1050105

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Actinoplanes rishiriensis NBRC 108556	GCA_016862375	contig	ncbi	1050105
66792	Actinoplanes rishiriensis strain NBRC 108556	1050105.3	wgs	patric	1050105

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	95	no
motile	yes	66.073	no
flagellated	no	88.964	no
gram-positive	yes	87.785	no
anaerobic	no	98.354	no
aerobic	yes	91.969	no
halophile	no	96.058	no
spore-forming	yes	89.14	no
thermophile	no	99.227	yes
glucose-util	yes	89.453	no
glucose-ferment	no	89.068	no

External links

@ref: 19173

culture collection no.: DSM 45866, BCC 49184, NBRC 108556

straininfo link

@ref: 87350
straininfo: 397359

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22354131	Actinoplanes rishiriensis sp. nov., a novel motile actinomycete isolated by rehydration and centrifugation method.	Yamamura H, Shimizu A, Nakagawa Y, Hamada M, Otoguro M, Tamura T, Hayakawa M	J Antibiot (Tokyo)	10.1038/ja.2012.8	2012	Actinobacteria/classification/genetics/isolation & purification, Actinomycetales/classification/genetics/isolation & purification, Hydrogen-Ion Concentration, Japan, Nucleic Acid Hybridization/methods, Phylogeny, RNA, Bacterial, RNA, Ribosomal, 16S/genetics, Sequence Analysis, RNA, *Soil Microbiology, Species Specificity	Enzymology
Phylogeny	26432564	Actinoplanes rhizophilus sp. nov., an actinomycete isolated from the rhizosphere of Sansevieria trifasciata Prain.	He H, Xing J, Liu C, Li C, Ma Z, Li J, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.000646	2015	Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonosporaceae/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sansevieria/microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry	Genetics
Metabolism	29974366	Actinoplanes deserti sp. nov., isolated from a desert soil sample.	Habib N, Khan IU, Chu X, Xiao M, Li S, Fang BZ, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1121-x	2018	Base Composition, Cell Wall/chemistry/metabolism, China, Desert Climate, Diaminopimelic Acid/metabolism, Fatty Acids/metabolism, Galactose/metabolism, Glucose/metabolism, Glycolipids/metabolism, Mannose/metabolism, Micromonosporaceae/classification/genetics/isolation & purification, Peptidoglycan/chemistry/metabolism, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/*genetics, Ribose/metabolism, Soil Microbiology, Spores, Bacterial/chemistry/growth & development, Vitamin K 2/metabolism, Xylose/metabolism	Phylogeny

Reference

@id	authors	catalogue	doi/url	title
19173	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45866)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-45866
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
87350	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID397359.1	StrainInfo: A central database for resolving microbial strain identifiers